Treemix

Notes & questions

• “Because we only use a single individual per taxon, we need to use the flag -noss. Otherwise, treemix will apply a correction for small sample size which is too conservative.” *ipyrad-analysis toolkit: treemix

Setup

Modified full results

• Removed several individuals/populations
  • Recent American/Australian composite breeds (Santa Gertrudis, Beefmaster, and Droughtmaster)
  • “East African Zebu” with quality issues in fastSTRUCTURE and PCA
• Consolidated several populations
  • All domestic yak breeds
  • All gayal populations
  • All Podolian Steppe breeds (Podolica, Maremmana, Boskarin, Sikias)
  • Combined Lowline Angus with Angus
  • Combined miniature Hereford with Hereford
• Removed all remaining populations with fewer than 5 individuals excluding Asian steppe breeds (Chaidamu Yellow) and the consolidated Podolian Steppe population

The resulting dataset has 2,167 individuals:

Base tree

m = 1

m = 2

Cattle only

• Same consolidations and removals as in full dataset, rooted with gayal

Base tree

m = 1

m = 2

Commentary